Tough Decisions Harsh Realities
by littlepatriot
Summary: This fanfic follows the thoughts and actions of numerous clones when they received Order 66. Meant to complement my previous Star Wars fanfic, "Forging a Family." Hugely AU.
1. Chapter 1

**Hey Folks! Sorry about the gap in writing. I've just finished up the 1****st**** semester of college and am now on Winter Break. I had this idea for this story in my head since I'd finished "Forging a Family" back in August. So…. here you go! – littleP **

**Chapter 1: Cody: **

Commander Cody didn't know what to feel, betrayal, anger, or sadness? His General, Obi Wan Kenobi had betrayed the Republic. The man who he'd thought fought for all that was good and righteous in the galaxy, was a traitor. Having the Chancellor comm him, ordering Executive Order 66 was not surprising, after all he was clone marshal commander. He knew as he listened to the Chancellor hand out his orders that he must obey, but seeing the grotesque features of the man's face along with his cruel voice made Cody's skin crawl underneath his armor.

After the comm blinked out of existence, Cody turned his gaze up and saw Obi Wan riding away on his mount, Boga, ignorant of the fate that his friend was about to bestow upon him. Friend, how unbidden the term came to his mind, Cody smiled grimly. He didn't think he could forget all the time he and Obi Wan spent together, on the battlefield, through thick and thin, they stuck together. The memories of many such times caused tears to well in Cody's eyes.

_Much more than a friend, a brother. _The gruff commander of the 212th Attack Battalion thought.

They were brothers, if not by blood, than by loyalty, and sacrifice. Cody had long ago realized that he could never kill one of his own brothers…. but he'd been given a direct order, one he must follow without question.

_But why!?_ A small voice cried out deep in his conscience.

His general had been one of the most loyal servants of the Republic he'd ever known, how could he have betrayed the very ideal he and the Jedi had been fighting to uphold? Obi Wan had spilt his blood for the Republic, and now he was plotting its downfall?

Doubt and suspicion began to worm its way into Cody's mind. He remembered the words the Republic Agent Regulan during the grand review by the Chancellor all those months ago, the bashful young agent telling the clones that they were sentients with a right to think for themselves. Another memory also came into his thoughts, one involving Kenobi himself. He remembered overhearing both Kenobi and Anakin Skywalker discussing that a Sith Lord had infiltrated the Senate.

_Could the Chancellor have been manipulated by the secret Sith? _It was a fair thought, but one that could wait. Right now he needed to focus on saving Obi Wan, his friend, his _brother, _from imminent destruction.

He knew that every other clone under his command, and likely every other clone in the Grand Army of the Republic had received the order, and were bent on carrying it out.

Frantically he commed his general, sweating buckets as he waited for Obi Wan to answer his call. When the man finally picked up the clone commander sighed in relief.

"General don't ask questions, just do as I tell you." Cody frantically said, speaking in a frantically rushed tone of voice. "I'm going to shoot you," Cody heard Obi Wan softly gasp, "you need to prepare yourself for the fall into the sinkhole."

Obi Wan was silent for a few seconds before replying. "While I have major reservations about this, I expect a full explanation when this is over, if I survive."

Cody smiled, Obi Wan sure knew how to make deadly situations brighter with his humor, however unintentional, a trait that Cody knew would haunt him if he were to kill his friend. "I would expect nothing less General Kenobi."

With that he shut of his comm, and gathered his wits about him before turning to the gunner near him.

"Blast him."

The gun let out a shriek of sound and a flash of blue light, the bolt impacting the wall near Kenobi.

Cody watched in silent hope and sickening horror as Kenobi and his mount fell, the latter letting out a high pitched whine as she fell into the all encompassing sinkhole.

"No!" An electric and static muffled voice yelled from behind the commander, shaking Cody from his thoughts.

Turning about, Cody found that Waxer, Wooley, and Boil were virtually running towards him, Waxer ran up and grabbed the commander by his shoulders and visibly shook him.

"Why'd you do it commander!? What happened to thinking for yourself? You're a dammed droid! You know the general is innocent! Something is very wrong here, sir." Waxer virtually mumbled every word he was speaking so fast.

Both Boil and Wooley, now in paratrooper armor, came up behind Waxer, on guard in case Cody tried anything.

Under his bucket, Cody raised his eyebrows. _Do they think I would have such little compassion towards my brother? _

"Cody," Wooley said, not bothering with formalities, "we know the general is innocent. Despite what the Chancellor has told us, the man is wrong, something is up, and I think it involves the Chancellor himself. Now I know why the Misfits are so suspicious of the man."

Cody smiled under his bucket at Wooley's gutsiness. _Openly disobeying an order, good man._ Cody thought with amusement, before his worry for Obi Wan flooded his mind once more.

"Men, it pleases me to see that I have the honor of serving with such loyal men." Cody noticed that the trio had gone stock still at his statement.

_I bet they weren't expecting this_. He thought grimly.

"I know the general is innocent, something is diffidently amiss, but I know that the Jedi would never betray the Republic that they have fought 3,000 years for. I informed the general of my intentions to blast him before hand; I can only think that it was the Force that caused the bolt to impact the wall rather than General Kenobi." Cody spoke in a calm, deep tone.

The three troopers were now slouched over in relief.

Cody was pleased that his most trusted men could count on him to do the just thing. "I want you three to go to the bottom of the sinkhole and retrieve our general. Once there, comm me, and try to get him to his star fighter unmolested, understood?"

"Sir yes sir!" The three clones snapped a salute and quickly went about rescuing their general.

Cody sighed in relief as he watched his general, his _brother, _and shoot off the planet. Needless to say, when Boil, Wooley, and Waxer had rescued Obi Wan, the Jedi Master was not a very happy person. Afterwards, Cody spent much time explaining to Obi Wan the situation and his actions earlier in the day. In return Obi Wan had shocked his commander by revealing the evidence that the Misfits had obtained through their various taps on the Chancellor.

Cody was seeing red as he learned that the man who led the Republic, was its biggest traitor.

Later that night, Cody was saddened when he learned of the massacre committed at the Jedi Temple.

_By brothers no doubt.  
><em> 

However, it gave him renewed strength to fight the newly born darkness that was sweeping the galaxy. Cody spent many hours going around to many of his men, telling them the facts, and showing them the evidence of the Chancellor's betrayal.

He was worried that many of his men would call him traitor for saying such things. However, he was immensely proud when he realized that nearly every one of his men would fight alongside him, and remain loyal to the Jedi. He and the 212th Attack Battalion would wait until their time was right to go rogue.

Early the next morning, he'd received the order to return to Coruscant, outwardly, Cody obeyed without question, however his thoughts were the exact opposite.

_I never thought I would be a rebel. _


	2. Rex

**Chapter 2: Rex **

Rex's mind was in complete and utter turmoil, but the words were being pulled from his throat like he was a pre programmed droid.

"Yes my lord." The 501st captain replied, the blue hologram of the Chancellor flickering out. Rex was left staring at the holocom held in his now shaking hands.

All of his thoughts immediately turned to Ahsoka, _his _Ahsoka. The Tortuga Jedi had become his world as of late, and dare he say it, his light.

And now he was supposed to extinguish that light without question or hesitation, but Rex hesitated. He couldn't harm, much less kill Ahsoka. It dawned on him that he would do anything to keep the young woman safe at any cost, even giving his life to save hers.

_Thank the maker that we're not on Coruscant with Appo._ A frown upturning his face underneath his helmet, he knew Appo would give the Jedi no remorse, and no mercy.

Rex, Ahsoka, and Torrent Company were on an unnamed moon in the Mid Rim, away from any large conglomerates of Republic Forces. Rex knew Order 66 would spread through the entire GAR, many Jedi would die, but here, on this small moon, Rex could try to save one.

_Not try, will. _Thinking of his men, Rex had confidence that Ahsoka would live on. Torrent Company, nearly all of them veterans, looked upon Ahsoka as a young sister. They'd grown attached to the young Jedi, they were brothers, and she was their sister, their _family_.

A sister, who laughed, cried, and bled with him and his men, she was no traitor.

Quickly snapping from his thoughts, Rex decided to turn such thoughts into actions. Rex knew that every other man in his company had received the message; he had to get to Ahsoka as quickly as possible, but in a discrete manner. Hurriedly walking towards his men, he saw Ahsoka standing on a small mound, looking out over the lush green landscape. Out of the corner of his eye he saw a "shinie" moving towards his Jedi, the man was a recruit picked up less than a month ago, no doubt completely loyal in every respect. A look of horror crossed over Rex's face, and he began to run towards the scene. The clone raised his blaster rifle at Ahsoka's back, the young Jedi turning around with a look of utter betrayal on her smooth face.

"Ahsoka!" Rex bellowed, he wouldn't get there in time…. she was going to die.

_If she dies it will be over my dead body. _Rex drew his dual blaster pistols in a flash, ready to put two bolts into the clone's head, but Rex was beaten to it.

A blaster pistol was shoved against the shinie's head with enough force to chip the white helmet, it's wielder ready to shoot.

"Put the rifle down Greaser, or I'll blast your head open." Kix, Torrent Company's medic growled. Behind him ARC Trooper Fives positioned himself with a clear shot at the clone's spine, ready to defend their beloved Jedi.

Veteran Torrent Company troopers swarmed around the scene, all preparing for a potential firefight. A trooper by the name of Dogma inserted himself in between Greaser's rifle and Ahsoka's body, protecting the young Jedi, who by now had taken out her lightsabers.

ARC trooper Echo also made his way into the scene, not wasting anytime, the commando wrapped an arm around Greaser's neck, while trooper Jesse wrenched Greaser's rifle away from his body. Rex and a few other troopers wrestled the recruit to the ground, and cuffed him.

"You're disobeying direct orders given from the Chancellor himself!" Greaser yelled, glaring at the veteran troopers who stood above him. "You're supposed to terminate the traitor! Follow your orders!"

"Ahsoka's no traitor shinie." Fives growled, fixing Greaser a glare that would melt durasteel.

"The Chancellor ordered all Jedi to be terminated! They've betrayed the Republic!" Greaser fired back, Ahsoka gasped in shock, eyes filled with tears. Rex moved around the group and stood near Ahsoka, grabbing her forearm lightly, trying to comfort her.

Greaser's helmet was slapped off his head, with a punch following a second later.

"Echo! Restrain yourself!" Rex demanded, the ARC trooper stepped away from the fallen rookie with a slight smirk of pleasure, his eyes filled with rage.

"If you speak of her like that again I will beat you to a pulp." A number of other clones joined in with silent murmurs of agreement. "The general has been nothing but loyal to the Republic, and us troopers. You haven't seen her in a single battle; I've been with her for years! Don't you dare demean someone like her again." Echo rumbled, cracking his gloved fists as he moved away.

"You're all insane! You may have me locked up for now, but when I get out, the Chancellor will have your heads for your betrayal." Greaser gave a short laugh and smiled towards Ahsoka.

That did it for Rex, with lightening speed; the clone captain knocked the recruit out with a punch to the face. The group of clones hauled the unconscious form of the recruit away, leaving just Ahsoka and Rex.

"Rex." Ahsoka whispered, a tear trailing down her cheeks "is it true that you were ordered to kill me? Are Jedi across the galaxy being killed by their men?" Ahsoka sounded desperate to know the answer.

Rex stared at her before he whispered back, "Yes."

That was all it took for the controlled young Jedi to break down, gasping for breath, with tears streaming down her face, Rex watched as the young woman's world crumbled.

Rex couldn't stand seeing Ahsoka like that, without thinking, he moved forward. Before he realized what he'd done, Ahsoka was in his arms, his gloved hands stroking her head.

"I'm so sorry Ahsoka." Rex spoke, his voice cracked with grief. He thought of all the other Jedi that he knew, Plo Koon, Yoda, Obi Wan, and Anakin, all were dead by now. "We can still get you out; we're not following the Chancellor's command."

Ahsoka's eyes widened in shock, looking up at her captain who'd grown to be her friend over the past couple of years.

"R…Rex, you would do such a thing? But you will be executed when you go back!" Ahsoka said, her arms wrapping tighter around Rex.

Rex smiled, touched by her concern. "We're not going back." He said flatly.

"What do you mean?" Ahsoka appeared stumped and confused by Rex's answer, it amused him.

"I mean Torrent Company isn't going back, we are loyal to the Republic, and the Republic owed itself to the Jedi Order's sacrifice. This order is nothing short of sanctioned mass murder, genocide. Torrent Company will never participate in an action against such innocent people, Jedi who nothing more than protect the government that now calls for their death." Rex spoke with no room for argument.

Ahsoka looked shocked, but not surprised by Rex's words, she'd known him since the war began. "But what about the rest of the men?" Ahsoka asked, still recovering from Rex's speech a few seconds earlier.

"You saw how the men reacted to Greaser's threat to you. I have no doubt many of the veterans will follow you and me. We will put the shinies on a ship headed back to Coruscant, and we will lay low for awhile. " Rex spoke with a tone of finality.

"Sir what do we do? We can't kill Ahsoka, and we can't go back to the GAR." Dogma asked the question in desperation.

"We lay low for awhile; hopefully other brothers like Smokes didn't follow the order as well." Rex reasoned, Commander Smokes was a hard head, but protected those he cared about, even if it meant disobeying orders.

The men of Torrent Company nodded their agreement and went to work readying for their departure.

Mere hours later, Torrent Company was headed off the moon. The loyal recruits were mind tricked by Ahsoka and put on a ship bound for the capital planet. Rex and the veterans of Torrent Company, along with Ahsoka boarded a ship. Looking out over the stars, Rex stood beside Ahsoka, the young Jedi who he'd seen grow from a teenager into a beautiful woman, and all be damned if he let her die. Rex and the men of Torrent Company would follow Ahsoka to hell and back.

He briefly heard a conversation going on behind him.

"Echo, do you think this means we're going to be rogue?" Fives asked his fellow ARC Trooper.

"I believe so Fives." Echo responded with a quiet amused grunt.

"I've always wondered what it would be like to live on the edge, now maybe we can finally get some excitement." Fives said with giddiness.

Rex could only smile.

-Greaser is my creation, all other characters belong to Lucas and Disney.


	3. Bly

**Chapter 3:Bly **

Aayla Secura. The name sparked memories of times past, she saving him on Maridun, and the numerous times they've discussed their future after the war was over.

_Not to be. _Bly thought grimly, having received the order to end Secura's life.

He sighed in regret, he didn't want to kill her, she had become not only his leader, but a close friend. A friend who listened to any and all his problems, and did all she could to solve them. Bly was proud to have her as a general.

Shaking his helmeted head slightly, his feelings washing away at the movement, he had to blast her.

He along with his lieutenants stood behind the general, all of them having received the order. Further from them, Bly knew that Galle would follow his orders regarding padawan Barriss Offee.

He looked back towards his general, his decision had been made. He had to follow his gut, and he was damn sure going to.

Pressing his hand to his helmet he activated the internal comm., opening up a channel with his men.

"Move up around behind her, you aim must be true men." Bly ordered his heart heavy.

His men moved into a circle behind General Secura and raised their blasters, preparing to shoot while the Jedi's back was turned.

Upon hearing the click of blasters being readied, Secura was startled.

It was all the opportunity Bly needed.

"Fire!" He roared into his comm.

Secura had no time to react, the bolts striking her body, twisting as she fell. Bly saw a glimpse of a frown upon her face; it caused his heart to ache. But, he had to do this.

Once Secura was lying on the damp soil motionless, Bly motioned to one of his men.

"Check her." He said gruffly, trying to hide the emotion in his voice.

The trooper moved towards and knelt down next to the unmoving forum.

"She's alive." The trooper said, sounding almost relieved.

Bly himself sighed in enormous relief, his plan had worked. He had to make her death look real, for the sake of the general, for the sake of his men, hell, for the sake of all of them.

"Good work lads." Bly praised his men, a smile forming on his chapped lips. Moving towards the still body of Aayla, Bly knelt down and gently cradled her head in his gloved hands. "Load her up, gently, I will contact Galle. We must be quick before others notice." The troopers nodded their agreement and set about following their orders. Bly moved away to make a quick holocall to his second in command.

"Yes sir?" Galle responded to Bly's message.

"Was your mission a success?" Bly questioned, hoping that his plan had worked fully.

"Yes it was sir, Offee is here… but she's a little upset." Bly could hear the amusement in the young clone's voice, Offee and Galle had grown close as of late.

Bly lightly chuckled at the implication. "You two report to our position, we must get off world as soon as possible. I will explain everything to Offee once Secura wakes."

"Sir yes sir!" Galle responded, giving a salute, before signing off.

"Sir what are we going to do." Bly turned around at the voice; his gaze fell upon Kinker, one of the only ones that had been with him from the beginning.

Putting a hand on Kinker's shoulder Bly replied, " Kinker we're going to do what we've always done, survive. Sure it may not me fun, but we will make it through this."

"But… but sir, I'm not ready to kill my brothers." Kinker said his voice sullen and sad.

Bly also thought of the action. Would he have to kill his brothers who saw the Jedi as a threat? He knew the answer was yes, but he wish it weren't. He cursed his brothers who couldn't see reason or freedom beyond the military bondage they'd been born into.

"Kinker, we may, but we can hold out hope that the lot of our brothers have seen reason and logic rather than follow orders blindly." Rex gave the clone a reassuring shake before letting his hand fall away.

"Alright sir, I hope so." Kinker said before walking off, in his mind, Bly hoped so too.

The 327th remained on Felucia until dusk, when Secura began to stir.

"Sir she's waking!" One of the medics shouted.

Bly, Galle, Offee, and a number of his other men ran over to the cot the Jedi was currently laying on.

She stirred for a few more moments before her eyes shot open and she gasped.

Bly was there immediately, pressing her gently back down onto the cot.

"General Secura! General you need to calm down! Aayla!", Bly shouted, that did the trick, her eyes widened in shock before she lay back down.

"Why?" She whispered hoarsely. The single word broke Bly's heart.

"Because I couldn't stand to see you die." Bly said truthfully. "Your death was ordered by the Chancellor himself, but I couldn't do it, none of us could."

The men around the cot nodded in agreement.

It was Offee who broke the silence.

"So why don't you tell us why you shot Aayla with stun bolts?" Her question was sharp with anger.

It was Galle who answered, much to Bly's relief.

"Because you along with any other Jedi in existence were just ordered to be killed, by your own men I may add. The Chancellor said it was because you'd betrayed the Republic, and no doubt, many of our brothers believed him. However, we Star Corps troopers hold no such view, you've fought with us for years and we've seen the Jedi lay their lives on the line like we clones do. It's impossible that those who fought for the Republic would betray it. We don't know what's going on, but we don't intend to kill our allies and friends." Even though his helmeted head, Galle's voice was full of pride and determination.

Offee smiled and patted the clone on his shoulder plate. "Thank you, all of you." She said, a smile as wide as a moon appearing on her face.

Bly felt encouraged, and gave a nod of his head. He looked down, taking off his helmet he stared into the depths of his general, his friend.

"General, I'm sorry." He croaked, overcome with emotion, even though it hadn't killed her, the sight of her men with blasters pointed towards her would stick with her, the thought made Bly shake.

A reassuring hand was put on his shoulder; Bly stilled and looked down in shock at the small smile upon Aayla's face. For a moment there was silence, only the faint rustling of Bly's kama was heard.

"Enough moping Bly," Secura said in a soft playful tone, "I'm still here, and am honored that you saved not only my life but that of my padawan as well, you went against your training. I'm proud, of all of you." Secura looked around, staring at each and every clone, giving them a look of reassurance and pride. "My boy's are the best." Secura said before lying gently back down.

The statement shocked all the clone's standing near, how General Secura referred to them, not as troopers, soldiers, but as boys. Her tone was almost that of a mother of older sister.

It suddenly dawned on Bly as it did the other members of the 327th Star Corps.

They were family, and nothing would break that.


End file.
